Atom 1 in the mol2 file has been assigned as type C.cat, which
presumably is causing the problem.

This atom is assigned type C.2 if I use the following command:

babel -ipdb in.pdb -omol2 out_h.mol2 -h

Is it that babel expects a space between the C.cat and the 1490?

If so, that still doesn't explain why I get different atom type
assignments using -p vs. -h. I know I can't use -p if I want the
charges in the output to be sensible (I assign them separately later),
but it's now looking like the -p option will also change atom types
...

Is it simply that the -p option is fully broken and I should just stop
using it?

Re: Fwd: OB writing non-standard atom types?

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